USPTO Patents Application 09533906

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LAW OFFICES

FiNNEGAN, Henderson,
Farabow, Garrett,
8 dunner,l.l.p.

I300 1 STREET, N. W.
WASHINGTON, D. C. 20O05
2O2-4^0S-'4OOO

construction of the term "amplifying" as being limited to non-specific amplification and entered
partial summary judgment accordingly.

Vysis contends that the court's decision is based, inter alia, on a profound
misunderstanding of the prosecution history of the '338 patent and has filed a motion seeking
entry of final judgment on the infiingement issue so that it can immediately appeal that ruling.
While Vysis does so, however, the trial court's ruling on this infringement issue should have no
effect on resolution of the patentability issues being addressed in these reissue proceedings.

In the first instance, the claim construction urged by Gen-Probe before the trial court is
flatly at odds with the claim construction it has advocated in this reissue proceeding, hi this
reissue proceeding, Gen-Probe filed a Protest against the claims of the '338 patent, asserting
invalidity over references that disclosed only specific amplification. For example, Gen-Probe
argued that claim 1 was anticipated by Powell et al.. Cell 50:831-840 (1987), a reference that
discloses PGR, perhaps the best known of the specific amplification methods. See Protest, pp.
23-25.

Second, the court's decision is currently a "partial simmiary judgment" that is not yet a
final, appealable court decision. Rule 54(b), Fed. R. Civ. P. The Patent Ovmer is presently
seeking to convert that order into a final judgment so that it can promptly appeal, but that relief
has not yet been granted. The Patent Owner will apprise the PTO of developments in this regard
as they occur.

Third, the court's decision is not a decision on the validity of the '338 patent. Lideed, the
court expressly recognized that "a motion for invalidity pursuant to 35 U.S.C. § 1 12 is not before
the Court." Order, p. 7, line 19. The court's decision is directed to issues of infringement and
does not control resolution of the issues of patentability that are currently before the PTO.

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LAW OFFICES

FINNECAN; HENDERSON,

Farabow, Garrett,
8 dunner,l.l.p.

1300 I STREET, N, W.
WASHINGTON, D. C, 20005
202-4-06-4000

Fourth, and perhaps most importantly, the court's decision is not logically compelling
because it is based on a manifest misunderstanding of the prosecution history of the original '338
patent that should be clear to the PTO even in advance of appellate review of that decision.
While it is true that the specification does not use the term "PGR," neither does it limit the
invention to non-specific amplification. The absence of any detailed discussion of amplification
methods is not remarkable because the inventors of the *338 patent had not invented
amplification. Both specific and non-specific amplification methods were well known in the art,
and the PTO so held repeatedly and without contradiction fi-om the Patent Owner in the original
prosecution, histead, the invention related to the combination of target capture with
amplification. That combination permits the use of non-specific primers for the amplification
step, but does not require the use of non-specific primers. And while the specification highlights
the benefits of the combination of target capture and non-specific amplification, it does not limit
the claimed combination to non-specific amplification.

The prosecution history of the '338 patent bears this out. Each of the five Examiners

who evaluated the appUcation and its related counterparts recognized that amplification

encompassed specific amplification as in PGR. Indeed, the substantive examination of the '338

patent began with a rejection for obviousness under 35 U.S.G. § 103 "over MulUs [the PGR

patent] when taken with any of Moss et al., Stabinsky or Engelhardt et al. and taken fiirther in

view of Ranki et al. or Josephson et al. or Schroder if necessary." See USSN 07/944,505, Office

Action of Nov. 5, 1992, at pp. 3-4. The Examiner explained that:

The primary reference teaches DNA amplification and point[s] out
the great value of this method for improved sensitivity as well as
improved ability to isolate specific nucleotide sequences. The
primary references do not specifically teach nucleic acid affinity
chromatography prior to the amplification reaction. The secondary
references all teach the well known method of affinity

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LAW OFFICES

FiNNECAN, Henderson,
Farabow, Garrett,
s dunner,l.l.p,

I300 I STREET, N. W.
WASHINGTON, D. C. 2000S
202-408-4000

chromatography. * * * It would be obvious for one of ordinary
skill in the art to combine the teachings of the primary references
which show improved sensitivity and improved ability to purify a
sequence with the secondary references which teach a method
providing improved ability to purify a sequence and improved
sensitivity since the methods are all directed to the same result and
one of ordinary skill would expect an improvement in results.

Id. That this was not 2i rejection alleging obviousness oi non-specific amplification is clear from
the separate treatment of dependent claims requiring non-specific amplification in that same
Office Action, based on a different technique which the PTO also characterized as "well known."
Id, at 4.

Of course, the inventors never distinguished the claims as not encompassing PGR, but

rather focused on the lack of any suggestion for the combination of PGR with target capture. See

USSN 08/283,080, Preliminary Amendment and Response to Restricfion Requirement of Dec. 5,

1995, pp. 11-12 and 15-20. The Examiners' beUef that the claims expressly covered PGR was

so fundamental to the examination that the Examiner who allowed the *338 Patent concluded in

the Statement of Reasons for Allowance that:

The claims are drawn to methods of PGR amplification
wherein the target is first separated from the sample by using a
support that binds to the target polynucleotide and then amplified.

* * *

[T]he art at the time of filing did not recognize that the efficiency
of PGR amplification would decrease due to the presence of
contaminants in a sample and therefore provided no motivation to
purify a target sample from a heterogeneous sample of nucleic
acids prior to amplification. Having not recognized the problem,
applicant's solution therefore, while utilizing routine methodology
to modify PGR amplification, would not have been obvious at the
time the invention was made.

USSN 08/238,080, Notice of Allowability of Oct. 13, 1997.

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Gen-Probe completely ignored this prosecution history in its opening brief in support of
its motion, but its reply brief urged that the PTO had not really rejected the claims as

encompassing PGR, as follows:

Vysis' initial applications were not rejected by the PTO because
Vysis' claims encompassed PGR, but because those claims were an
"obvious" attempt to achieve the same result as PGR in a different
manner.

Gen-Probe's Reply Memorandum, p. 14. The trial court accepted this contention, holding:

Gen-Probe asserts that the rejection by the PTO of the
patent application based on the MuUis (PGR) patent does not
support the claim that the patent covered PGR amphfication
methods. Vysis acknowledged in oral argument that [it] did not
have a license to the Mullis patents or PGR method. Gen-Probe
argues that the patent application was rejected as obvious in light
of the PGR patents because specific capture methods plus non-
specific amplification were an attempt to achieve the same results
as PGR

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The Gourt concludes that the references to the Mullis
patents and PGR in the prosecution history do not help clarify the
proper construction of the term "amplifying" as used in the '338
patent. At most, the prosecution history indicates that the idea of
amplification by first using specific target capture techniques is
close enough to the goals of PGR to be "obvious" to the PTO in
light of the Mullis patents. [Footnote omitted.]

Slip op. at 8-9. The Statement of Reasons for Allowance and the separate treatment of claims

directed to non-specific amplification demonstrate the error in Gen-Probe's contention and the

court's holding. It could not be clearer that the '338 patent claims were repeatedly rejected

precisely because they encompassed specific amplification techniques such as PGR. The court's
holding is manifestly based, at least in part, on a fundamental misunderstanding of the

LAW OFFICES

FiNNECAN, Henderson,
Farabow, Garrett,

S DUlsINER,L.L.P.

I300 1 STREET, N. W.
WASHINGTON, D. C. 20005
202-4-O8-4O00

prosecution history.

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In order to avoid any ambiguity as to the scope of the amplification techniques
encompassed by the claims, the Patent Owner wishes to add to its previously submitted
intermediate scope claims dependent claims that recite "random primers" and "specially tailored
primers." These amendments are made in the accompanying Supplemental Preliminary
Amendment and are fully supported by the original specification.

If there are any fees due with the fihng of this Notice not already accounted for, please

charge the fees to our Deposit Account No. 06-0916

Respectfully submitted,

FINNEGAN, HENDERSON, FARABOW,
GARRETT & DUNNER, L.L.P.

Dated: July 16, 2001

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Jean B. Fordis
Reg. No. 32,984

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LAW OFFICES

FlNNECAN, HENDERSON,

Farabow, Garrett,
s dunner, l.l.p.

I300 I STREET, N. W.
WASHINGTON, D. C. 20005
202-408-A000

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